Paper Citing NAMD - Abstract
Luan, Binquan; Aksimentiev, Aleksei
Control and reversal of the electrophoretic force on DNA in a charged nanopore
JOURNAL OF PHYSICS-CONDENSED MATTER, 22 Art. No. 454123, NOV 17 2010
Electric field driven transport of DNA through solid-state nanopores is the key process in nanopore-based DNA sequencing that promises dramatic reduction of genome sequencing costs. A major hurdle in the development of this sequencing method is that DNA transport through the nanopores occurs too quickly for the DNA sequence to be detected. By means of all-atom molecular dynamics simulations, we demonstrate that the velocity of DNA transport through a nanopore can be controlled by the charge state of the nanopore surface. In particular, we show that the charge density of the nanopore surface controls the magnitude and/or direction of the electro-osmotic flow through the nanopore and thereby can significantly reduce or even reverse the effective electrophoretic force on DNA. Our work suggests a physical mechanism to control DNA transport in a nanopore by chemical, electrical or electrochemical modification of the nanopore surface.
